added fits_to_png functionality

atdb_statistics/atdb_plot.py

@@ -5,6 +5,7 @@
     Description: atdb plot module
 """
 
+import os
 import datetime
 import plotly
 import plotly.graph_objs as go
@@ -544,3 +545,38 @@ def do_time_used_science_pie_plot(title, subtitle, data):
     plt.legend(loc='upper right')
 
     plt.show()
+
+
+def fits_to_png_apercal(input_file_name,output_file_name):
+    import matplotlib.pyplot as plt
+    from astropy.wcs import WCS
+    from astropy.io import fits
+    import matplotlib.colors as mc
+    output = output_file_name
+    fits_file = input_file_name
+    # open continuum image
+    fits_hdulist = fits.open(fits_file)
+    # get WCS header of cube
+    wcs = WCS(fits_hdulist[0].header)
+    # remove unnecessary axis
+    if wcs.naxis == 4:
+        wcs = wcs.dropaxis(3)
+        wcs = wcs.dropaxis(2)
+        img = fits_hdulist[0].data[0][0]
+    elif wcs.naxis == 3:
+        wcs = wcs.dropaxis(2)
+        img = fits_hdulist[0].data[0]
+    else:
+        img = fits_hdulist[0].data
+    # set up plot
+    ax = plt.subplot(projection=wcs)
+    # add image using sym-log scaling
+    fig = ax.imshow(img * 1.e3, norm=mc.SymLogNorm(1.e-9, vmin=0.03, vmax=200), origin='lower')
+    # add colorbar
+    cbar = plt.colorbar(fig)
+    cbar.set_label('Flux Density [mJy/beam]')
+    ax.coords[0].set_axislabel('Right Ascension')
+    ax.coords[1].set_axislabel('Declination')
+    ax.coords[0].set_major_formatter('hh:mm')
+    ax.set_title("{0:s}".format(os.path.basename(fits_file)))
+    plt.savefig(output, overwrite=True, bbox_inches='tight', dpi=300)
\ No newline at end of file

atdb_stats.py

@@ -310,8 +310,9 @@ def do_times(args):
         if result['ingest_speed'] is not None and result['ingest_speed'] > 0:
             datapoint = {}
             datapoint['taskid'] = result['taskID']
-            nofrag,frag = result['timestamp_ingesting'].split('.')
-            timestamp = datetime.datetime.strptime(nofrag, '%Y-%m-%dT%H:%M:%S')
+            # nofrag,frag = result['timestamp_ingesting'].split('.')
+            # timestamp = datetime.datetime.strptime(nofrag, '%Y-%m-%dT%H:%M:%S')
+            timestamp = datetime.datetime.strptime(result['timestamp_ingesting'], '%Y-%m-%dT%H:%M:%SZ')
             datapoint['timestamp'] = timestamp
             datapoint['type'] = 'ingesting'
             datapoint['duration'] = result['ingest_duration']
@@ -325,8 +326,9 @@ def do_times(args):
         if result['timestamp_ingest_error'] is not None:
             datapoint = {}
             datapoint['taskid'] = result['taskID']
-            nofrag,frag = result['timestamp_ingest_error'].split('.')
-            timestamp = datetime.datetime.strptime(nofrag, '%Y-%m-%dT%H:%M:%S')
+            # nofrag,frag = result['timestamp_ingest_error'].split('.')
+            # timestamp = datetime.datetime.strptime(nofrag, '%Y-%m-%dT%H:%M:%S')
+            timestamp = datetime.datetime.strptime(result['timestamp_ingest_error'], '%Y-%m-%dT%H:%M:%SZ')
             datapoint['timestamp'] = timestamp
             datapoint['type'] = 'ingest_error'
             datapoint['speed_bps'] = prev_ingest_speed
@@ -515,6 +517,12 @@ def main():
     parser.add_argument("--interval",
                         default="day",
                         help="Shows bars per interval. Possible options: minute, hour, day, month")
+    parser.add_argument("--input_filename","-i",
+                        default="",
+                        help="input filename")
+    parser.add_argument("--output_filename","-o",
+                        default="",
+                        help="output filename")
     # plot parameters
     parser.add_argument("--title",
                         default="Title",
@@ -534,6 +542,12 @@ def main():
     parser.add_argument("--colormap",
                         default="viridis",
                         help="see: https://matplotlib.org/examples/color/colormaps_reference.html")
+
+    # commands
+    parser.add_argument("--fits2png",
+                        default=False,
+                        help="convert FITS to PNG.",
+                        action="store_true")
     # All parameters in a file
     parser.add_argument('--argfile',
                         nargs='?',
@@ -544,15 +558,16 @@ def main():
                         help="Show current version of this program.",
                         action="store_true")
 
+
     args = get_arguments(parser)
 
     # --------------------------------------------------------------------------------------------------------
     if (args.version):
-        print('--- atdb_stats.py - version 1.0.0 - 9 jun 2019 ---')
+        print('--- atdb_stats.py - version 1.1.0 - 25 nov 2019 ---')
         print('Copyright (C) 2019 - Nico Vermaas - ASTRON. This program comes with ABSOLUTELY NO WARRANTY;')
         return
 
-    print('--- atdb_stats.py - version 1.0.0 - 9 jun 2019 ---')
+    print('--- atdb_stats.py - version 1.1.0 - 25 nov 2019 ---')
     print('Copyright (C) 2019 - Nico Vermaas - ASTRON. This program comes with ABSOLUTELY NO WARRANTY;')
     if args.starttime != None:
         starttime = datetime.datetime.strptime(args.starttime, TIME_FORMAT)
@@ -604,6 +619,9 @@ def main():
     elif presentation=="time_used":
        do_time_used(args)
 
+    elif args.fits2png:
+        atdb_plot.fits_to_png_apercal(args.input_filename,args.output_filename)
+
     if args.remote_post_command != None:
         execute_remote_command(args.atdb_host, args.remote_post_command)
 

data/fits_to_png.args

+--fits2png
+--input_file=D:\my_happili\image_mf_04.fits
+--output_file=D:\my_happili\image_mf_04.png

data/sky.args

@@ -7,4 +7,4 @@
 --plot_type=scatter
 --colormap=viridis
 --starttime=2018-01-01 00:00
---endtime=2019-06-17 00:00
+--endtime=2019-11-12 00:00

data/time_used_science_pie_aug2019_prod.args

+--presentation=time_used
+--atdb_host=http://192.168.22.22/atdb
+--title=APERTIF Science Pie - Aug 2019
+--query=from=2019-08-01T00:01:00Z&to=2019-09-01T00:00:00Z&report_type=time_used_science_pie
\ No newline at end of file

data/time_used_science_pie_aug2019_vm.args

+--presentation=time_used
+--atdb_host=http://192.168.22.22/atdb
+--title=APERTIF Science Pie - Aug 2019
+--query=from=2019-08-01T00:01:00Z&to=2019-09-01T00:00:00Z&report_type=time_used_science_pie
\ No newline at end of file

data/time_used_system_pie_aug2019_prod.args

+--presentation=time_used
+--atdb_host=http://atdb.astron.nl/atdb
+--title=APERTIF System Pie - Aug 2019
+--query=from=2019-08-01T00:01:00Z&to=2019-09-01T00:00:00Z&report_type=time_used_system_pie
\ No newline at end of file

data/time_used_system_pie_jul2019_prod.args

+--presentation=time_used
+--atdb_host=http://atdb.astron.nl/atdb
+--title=APERTIF System Pie - Aug 2019
+--query=from=2019-08-01T00:01:00Z&to=2019-08-31T00:08:00Z&report_type=time_used_system_pie
\ No newline at end of file

data/times_today_prod.args

 --presentation=times
 --atdb_host=http://atdb.astron.nl/atdb
 --title=I/O speeds from ATDB
---subtitle=18 - 23 july 2019
+--subtitle=29/30 aug 2019
 --y_axis_title=I/O Speed in Gbps
---query=starttime__gt=2019-07-18T00:00:00Z&starttime__lt=2019-07-23T00:00:00Z
+--query=starttime__gt=2019-08-29T00:00:00Z&starttime__lt=2019-09-02T00:00:00Z